InDesign's QR code generator creates v2.1 vCard data, which does not recognize most accented characters. (It is a somewhat outdated, limited-function implementation.)
The solution is to use another QR code generator that supports v3.0 vCard, or to "hand code" your vCard data in a text field. Wikipedia has a pretty good breakdown of the field types, codes, etc. and there are other resources out there.
| Word & InDesign to Kindle & EPUB: a Pro Guide (Amazon)